In the context of plant and animal production, prophylaxis consists of developing and using a set of practices to prevent the appearance of health problems, often of multifactorial origin.

In plant production, prophylaxis, the cornerstone of agroecological crop protection, aims to prevent the development of diseases, pests and weeds, using a combination of physical, chemical, (micro)biological and/or genetic practices. They can act directly against bio-aggressors or seek to make better use of beneficial agrobiodiversity (crop auxiliaries) in order to disrupt their biological cycles. Among these practices, the ones most used by farmers are crop rotation, (micro)biological control, the use of resistant cultivars, seed sorting and equipment cleaning.

Prophylaxis is also one of the pillars of integrated management of animal health and disease prevention. It is part of a holistic approach that seeks to reduce health hazards and stimulate the individual and the collective immunities. Prevention takes into account the different causes of disease outbreaks, such as transmission vectors and rearing conditions (housing, population density, feed, microbiome, etc.), while respecting the health (broad sense) of animals in order to ensure their well-being. Biosecurity and good hygiene practices in animal husbandry aim to prevent the development of pathogenic agents without impairing the development of benign and beneficial microorganisms. The onset of transmissible diseases can be prevented by vaccination, screening and/or isolation of sick conspecifics. Non-transmissible diseases, such as pododermatitis, are caused by changes in production methods. It is possible to improve the environment in which animals live, or to favor animals with robustness and/or resistance/tolerance to disease, either by choosing robust breeds or by genetic selection of populations.

Prophylaxis is part of the development of sustainable agriculture based on systems that are more flexible because they anticipate the issues better, and mobilize practices linked to agroecology.